Statistics Summary Report for BSGC Center

Last updated: Feb 2 2012

• Target Status Statistics
• Table 1: Status Statistics for BSGC
• Table 2: Status Statistics for BSGC by Organisms
• Deposited Structure Statistics
• Table 3: PDB Status Statistics for Structures from BSGC
• Table 4: List of Structures Deposited by BSGC in the PDB
• Sequence Redundancy Statistics
• Table 5: Sequence Redundancy Statistics for BSGC by Experimental Status
• Table 6: Sequence Redundancy Statistics for Structures Released by BSGC in the PDB by Year

Target Status Statistics

Total number of targets deposited by BSGC to TargetDB: 1036

      View BSGC Target List

Table 1: Status Statistics for BSGC

Status	Total Number of Targets	(%) Relative to "Cloned" Targets	(%) Relative to "Expressed" Targets	(%) Relative to "Purified" Targets	(%) Relative to "Crystallized" Targets
Cloned	900	100.0	-	-	-
Expressed	600	66.7	100.0	-	-
Soluble	423	47.0	70.5	-	-
Purified	242	26.9	40.3	100.0	-
Crystallized	96	10.7	16.0	39.7	100.0
Diffraction-quality Crystals	72	8.0	12.0	29.8	75.0
Diffraction	66	7.3	11.0	27.3	68.8
NMR Assigned	47	5.2	7.8	19.4	-
HSQC	22	2.4	3.7	9.1	-
Crystal Structure	59	6.6	9.8	24.4	61.5
NMR Structure	4	0.4	0.7	1.7	-
In PDB1	62	6.9	10.3	25.6	61
Work Stopped	755	-	-	-	-
Test Target	0	-	-	-	-
Other	0	-	-	-	-

Last updated: Feb 2 2012

Note 1:   Number of targets with status "in PDB" may not be equal to number of structures determined by a project. A target may reference several PDB IDs (example: structure of the same polypeptides with different ligands). Multiple targets in TargetDB may identify the same PDB structure when a stucture is a result of collaboration between different centers and each center includes the target on its target list.

Table 2: Status Statistics for BSGC by Organism

These statistics are derived from mapping of target sequences to GenBank using >=98% sequence identity cut off.

Organism	Total Number1	Work Stopped	Cloned	Expressed	Purified	Crystallized	Crystal Structure	NMR Structure	In PDB
Archaea	208	146	188	121	60	28	17	1	18
Bacteria	797	579	682	465	181	68	42	3	44
Prokaryota	1005	725	870	586	241	96	59	4	62

Last updated: Feb 2 2012

Note 1:   Total counts in this table may differ from total number of targets and structures. A target is counted in different organism specifications if:
- a target is mapped to different organisms
- a target is a hybrid complex (for example:a complex of human and mouse polypeptides).

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Deposited Structure Statistics for BSGC Center

Number of Released X-Ray Structures: 85

Number of Released NMR Structures: 3

Total number of released structures from BSGC center in the PDB: 88

Table 3: PDB Status Statistics for Structures from BSGC

PDB Status	Number of Structures
Total Deposited	88
Released	88
In Process	0

Last updated: Feb 2 2012

Note 1:   "Total Deposited" are all structures in the PDB including structures released to the public and structures that are in the process to be released ("Released on Publication" , "Released on Certain Date", etc.).

Table 4: List of Structures Deposited in the PDB by BSGC

Total number of structures: 88

Structures of distinct targets: 601

1   A target may reference several PDB IDs (example: structure of the same polypeptides with different ligands).
In this case only one structure is counted to compute number of structures of distinct targets.

Related PDB_ID(s): PDB_ID(s) associated with the same target in TargetDB.

PDB_ID	Title	Target_id	Deposition Date	Released Date	PDB Status	Related PDB_ID in TargetDB
1TD9	crystal structure of a phosphotransacetylase from bacillus subtilis	BSGCAIR30616	2004-05-21	2004-12-07	REL	1XCO
2MJP	structure-based identification of the biochemical function of a hypothetical protein from methanococcus jannaschii:mj0226	BSGCAIR30511	1999-01-27	2000-01-28	REL	none
1SU2	crystal structure of the nudix hydrolase dr1025 in complex with atp	BSGCAIR30561	2004-03-26	2004-05-11	REL	none
1F5S	crystal structure of phosphoserine phosphatase from methanococcus jannaschii	BSGCAIR30380	2000-06-15	2001-06-20	REL	1J97 1L7M 1L7N 1L7O 1L7P
1G8A	pyrococcus horikoshii fibrillarin pre-rrna processing protein	BSGCAIR30655	2000-11-16	2003-10-14	REL	none
1L7N	transition state analogue of phosphoserine phosphatase (aluminum fluoride complex)	BSGCAIR30380	2002-03-16	2002-06-19	REL	none
1T6Y	crystal structure of adp, amp, and fmn bound tm379	BSGCAIR30409	2004-05-07	2004-08-10	REL	none
2I1O	crystal structure of a nicotinate phosphoribosyltransferase from thermoplasma acidophilum	BSGCAIR30619	2006-08-14	2006-08-29	REL	none
1T71	crystal structure of a novel phosphatase mycoplasma pneumoniaefrom	BSGCAIR30460	2004-05-07	2004-12-07	REL	none
2I15	crystal structure of mpn423 from mycoplasma pneumoniae	BSGCAIR30378	2006-08-12	2006-10-10	REL	none
1L2F	crystal structure of nusa from thermotoga maritima: a structure-based role of the n-terminal domain	BSGCAIR30412	2002-02-20	2003-09-23	REL	none
1SUM	crystal structure of a hypothetical protein at 2.0 a resolution	BSGCAIR30480	2004-03-26	2004-08-24	REL	none
1SU0	crystal structure of a hypothetical protein at 2.3 a resolution	BSGCAIR30592	2004-03-25	2004-08-24	REL	none
2HYB	crystal structure of hexameric dsrefh	BSGCAIR31214 BSGC:BSGCAIR31215 BSGC:BSGCAIR31216	2006-08-04	2007-07-03	REL	none
1S4M	crystal structure of flavin binding to fad synthetase from thermotoga maritina	BSGCAIR30409	2004-01-16	2004-10-19	REL	none
2HY5	crystal structure of dsrefh	BSGCAIR31214 BSGC:BSGCAIR31215 BSGC:BSGCAIR31216	2006-08-04	2006-09-19	REL	2HYB
1RQ0	crystal structure of peptide releasing factor 1	BSGCAIR30383	2003-12-03	2004-08-17	REL	none
1OZ9	crystal structure of aq_1354, a hypothetical protein from aquifex aeolicus	BSGCAIR30418	2003-04-08	2003-09-23	REL	none
1OY5	crystal structure of trna (m1g37) methyltransferase from aquifex aeolicus	BSGCAIR30419	2003-04-03	2003-11-11	REL	none
1Q8C	a conserved hypothetical protein from mycoplasma genitalium shows structural homology to nusb proteins	BSGCAIR30482	2003-08-20	2003-09-30	REL	none
2HQL	crystal structure of a small single-stranded dna binding protein from mycoplasma pneumoniae	BSGCAIR30666	2006-07-18	2007-05-01	REL	none
1L7P	substrate bound phosphoserine phosphatase complex structure	BSGCAIR30380	2002-03-16	2002-06-19	REL	none
1S3M	structural and functional characterization of a novel archaeal phosphodiesterase	BSGCAIR30314	2004-01-13	2004-08-10	REL	none
2HQB	crystal structure of a transcriptional activator of comk gene from bacillus halodurans	BSGCAIR31267	2006-07-18	2007-05-29	REL	none
1SZ3	crystal structure of nudix hydrolase dr1025 in complexed with gnp and mg+2	BSGCAIR30561	2004-04-02	2004-05-11	REL	none
1TD6	crystal structure of the conserved hypothetical protein mp506/mpn330 (gi: 1674200)from mycoplasma pneumoniae	BSGCAIR30529	2004-05-21	2004-12-07	REL	none
1S7D	crystal structure of refined tetragonal crystal of yoda from escherichia coli	BSGCAIR30656	2004-01-29	2004-08-10	REL	none
1Z0U	crystal structure of a nad kinase from archaeoglobus fulgidus bound by nadp	BSGCAIR30424	2005-03-02	2005-04-19	REL	none
1NZ0	rnase p protein from thermotoga maritima	BSGCAIR30512	2003-02-14	2003-06-24	REL	none
1T8B	crystal structure of refolded phou-like protein (gi 2983430) from aquifex aeolicus	BSGCAIR30415	2004-05-11	2004-12-07	REL	none
1T6S	crystal structure of a conserved hypothetical protein from chlorobium tepidum	BSGCAIR30640	2004-05-07	2004-12-07	REL	none
1N0F	crystal structure of a cell division and cell wall biosynthesis protein upf0040 from mycoplasma pneumoniae: indication of a novel fold with a possible new conserved sequence motif	BSGCAIR30390	2002-10-13	2003-10-21	REL	none
1JX7	crystal structure of ychn protein from e.coli	BSGCAIR30513	2001-09-05	2002-09-07	REL	none
1LFP	crystal structure of a conserved hypothetical protein aq1575 from aquifex aeolicus	BSGCAIR30373	2002-04-11	2002-06-19	REL	none
1S12	crystal structure of tm1457	BSGCAIR30477	2004-01-05	2004-12-07	REL	none
2HEK	crystal structure of o67745, a hypothetical protein from aquifex aeolicus at 2.0 a resolution.	BSGCAIR30544	2006-06-21	2006-07-04	REL	none
1NF2	x-ray crystal structure of tm0651 from thermotoga maritima	BSGCAIR30381	2002-12-12	2003-09-16	REL	none
1YT5	crystal structure of nad kinase from thermotoga maritima	BSGCAIR30585	2005-02-09	2005-04-05	REL	none
1MRZ	crystal structure of a flavin binding protein from thermotoga maritima, tm379	BSGCAIR30409	2002-09-19	2003-09-23	REL	1S4M 1T6X 1T6Y 1T6Z 2I1L
1SBQ	crystal structure of methenyltetrahydrofolate synthetase from mycoplasma pneumoniae at 2.2 resolution	BSGCAIR30461	2004-02-10	2004-08-10	REL	1U3F 1U3G
1JEO	crystal structure of the hypothetical protein mj1247 from methanococcus jannaschii at 2.0 a resolution infers a molecular function of 3-hexulose-6-phosphate isomerase.	BSGCAIR30509	2001-06-18	2002-02-20	REL	none
1T6Z	crystal structure of riboflavin bound tm379	BSGCAIR30409	2004-05-07	2004-08-10	REL	none
1TM9	nmr structure of gene target number gi3844938 from mycoplasma genitalium: berkeley structural genomics center	BSGCAIR30548	2004-06-10	2004-08-10	REL	none
1T72	crystal structure of phosphate transport system protein phou from aquifex aeolicus	BSGCAIR30415	2004-05-07	2004-12-07	REL	1T8B
2I14	crystal structure of nicotinate-nucleotide pyrophosphorylase from pyrococcus furiosus	BSGCAIR30636	2006-08-12	2006-10-10	REL	none
1PA4	solution structure of a putative ribosome-binding factor from mycoplasma pneumoniae (mpn156)	BSGCAIR30410	2003-05-13	2004-03-02	REL	none
1XCO	crystal structure of a phosphotransacetylase from bacillus subtilis in complex with acetylphosphate	BSGCAIR30616	2004-09-02	2004-12-07	REL	none
1Z0Z	crystal structure of a nad kinase from archaeoglobus fulgidus in complex with nad	BSGCAIR30424	2005-03-02	2005-04-26	REL	none
1STZ	crystal structure of a hypothetical protein at 2.2 a resolution	BSGCAIR30318	2004-03-25	2004-08-24	REL	none
1T6X	crystal structure of adp bound tm379	BSGCAIR30409	2004-05-07	2004-08-10	REL	none
2I1L	crystal structure of the c2 form of fad synthetase from thermotoga maritima	BSGCAIR30409	2006-08-14	2006-11-07	REL	none
1S7O	crystal structure of putative dna binding protein sp_1288 from streptococcus pygenes	BSGCAIR30594	2004-01-29	2004-06-29	REL	none
1YTE	crystal structure of a nicotinate phosphoribosyltransferase from thermoplasma acidophilum, phosphoribosylpyrophosphate bound structure	BSGCAIR30619	2005-02-10	2005-03-08	REL	none
1N0G	crystal structure of a cell division and cell wall biosynthesis protein upf0040 from mycoplasma pneumoniae: indication of a novel fold with a possible new conserved sequence motif	BSGCAIR30390	2002-10-13	2003-10-21	REL	none
1SUW	crystal structure of a nad kinase from archaeoglobus fulgidus in complex with its substrate and product: insights into the catalysis of nad kinase	BSGCAIR30424	2004-03-26	2004-08-24	REL	1Z0S 1Z0U 1Z0Z
1U3F	structural and functional characterization of a 5,10-methenyltetrahydrofolate synthetase from mycoplasma pneumoniae (gi: 13508087)	BSGCAIR30461	2004-07-21	2004-12-07	REL	none
1S3L	structural and functional characterization of a novel archaeal phosphodiesterase	BSGCAIR30314	2004-01-13	2004-08-10	REL	1S3M 1S3N
1T70	crystal structure of a novel phosphatase from deinococcus radiodurans	BSGCAIR30429	2004-05-07	2004-12-07	REL	none
1S7C	crystal structure of mes buffer bound form of glyceraldehyde 3-phosphate dehydrogenase from escherichia coli	BSGCAIR30560	2004-01-29	2004-08-10	REL	none
1R5J	crystal structure of a phosphotransacetylase from streptococcus pyogenes	BSGCAIR30593	2003-10-10	2004-04-13	REL	none
1SJY	crystal structure of nudix hydrolase dr1025 from deinococcus radiodurans	BSGCAIR30561	2004-03-04	2004-05-11	REL	1SOI 1SU2 1SZ3
2BA2	crystal structure of the duf16 domain of mpn010 from mycoplasma pneumoniae	BSGCAIR30905	2005-10-13	2006-03-07	REL	none
1MGP	hypothetical protein tm841 from thermotoga maritima reveals fatty acid binding function	BSGCAIR30341	2002-08-15	2002-09-18	REL	none
1U0L	crystal structure of yjeq from thermotoga maritima	BSGCAIR31221	2004-07-13	2004-09-07	REL	none
1S3N	structural and functional characterization of a novel archaeal phosphodiesterase	BSGCAIR30314	2004-01-13	2004-08-10	REL	none
1SOI	crystal structure of nudix hydrolase dr1025 in complex with sm+3	BSGCAIR30561	2004-03-15	2004-05-11	REL	none
1G2I	crystal structure of a novel intracellular protease from pyrococcus horikoshii at 2 a resolution	BSGCAIR30332	2000-10-19	2000-11-08	REL	none
1DUS	mj0882-a hypothetical protein from m. jannaschii	BSGCAIR30382	2000-01-18	2000-07-19	REL	none
1MJH	structure-based assignment of the biochemical function of hypothetical protein mj0577: a test case of structural genomics	BSGCAIR30507	1998-11-04	1998-12-23	REL	none
1L7M	high resolution liganded structure of phosphoserine phosphatase (pi complex)	BSGCAIR30380	2002-03-15	2002-04-03	REL	none
1J97	phospho-aspartyl intermediate analogue of phosphoserine phosphatase	BSGCAIR30380	2001-05-24	2001-07-25	REL	none
1ZXJ	crystal structure of the hypthetical mycoplasma protein, mpn555	BSGCAIR30355	2005-06-08	2005-07-26	REL	none
1YTD	crystal structure of a nicotinate phosphoribosyltransferase from thermoplasma acidophilum, native structure	BSGCAIR30619	2005-02-10	2005-03-08	REL	1YTE 1YTK 2I1O
1Z0S	crystal structure of an nad kinase from archaeoglobus fulgidus in complex with atp	BSGCAIR30424	2005-03-02	2005-04-19	REL	none
1SHS	small heat shock protein from methanococcus jannaschii	BSGCAIR30505	1998-07-30	1999-07-30	REL	none
1FO5	solution structure of reduced mj0307	BSGCAIR30506	2000-08-24	2001-04-11	REL	none
1U3G	structural and functional characterization of a 5,10-methenyltetrahydrofolate synthetase from mycoplasma pneumoniae (gi: 13508087)	BSGCAIR30461	2004-07-21	2004-12-07	REL	none
1YTK	crystal structure of a nicotinate phosphoribosyltransferase from thermoplasma acidophilum with nicotinate mononucleotide	BSGCAIR30619	2005-02-10	2005-03-08	REL	none
1NYE	crystal structure of osmc from e. coli	BSGCAIR30339	2003-02-12	2004-03-02	REL	none
1FBN	crystal structure of a fibrillarin homologue from methanococcus jannaschii, a hyperthermophile, at 1.6 a	BSGCAIR30365	1999-04-25	2000-04-26	REL	none
1YF2	three-dimensional structure of dna sequence specificity (s) subunit of a type i restriction-modification enzyme and its functional implications	BSGCAIR30591	2004-12-30	2005-02-15	REL	none
1ILW	crystal structure of pyrazinamidase/nicotinamidase of pyrococcus horikoshii	BSGCAIR30510	2001-05-08	2001-12-12	REL	none
1L7O	crystal structure of phosphoserine phosphatase in apo form	BSGCAIR30380	2002-03-16	2002-06-19	REL	none
1T75	crystal structure of escherichia coli beta carbonic anhydrase	BSGCAIR31213	2004-05-07	2004-06-22	REL	none
1EKE	crystal structure of class ii ribonuclease h (rnase hii) with mes ligand	BSGCAIR30321	2000-03-07	2000-09-13	REL	none
1LQL	crystal structure of osmc like protein from mycoplasma pneumoniae	BSGCAIR30348	2002-05-10	2003-08-05	REL	none
2EIF	eukaryotic translation initiation factor 5a from methanococcus jannaschii	BSGCAIR30508	1998-10-12	1999-10-12	REL	none
1N0E	crystal structure of a cell division and cell wall biosynthesis protein upf0040 from mycoplasma pneumoniae: indication of a novel fold with a possible new conserved sequence motif	BSGCAIR30390	2002-10-13	2003-10-21	REL	1N0F 1N0G

Last updated: Feb 2 2012

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Sequence Redundancy Statistics

Table 5: Sequence Redundancy Statistics for BSGC by Experimental Status

Sequence Identity(%)	Novel Targets Status: Selected	Novel Targets Status: Cloned	Novel Targets Status: Expressed	Novel Targets Status: Purified	Novel Targets Status: Crystallized	Novel Targets Status: Crystal Structure	Novel Targets Status: NMR Structure	Novel Targets Status: in PDB
<100	854	758	522	231	95	59	4	62
<98	1029	753	520	231	95	59	4	62
<95	842	747	516	230	95	59	4	62
<90	830	736	514	229	95	59	4	62
<70	736	662	479	220	94	59	4	62
<50	515	472	369	185	89	57	4	60
<40	408	379	295	170	82	56	4	59
<30	240	240	210	140	72	54	4	57

Last updated: 12-01-10

Sequence redundancy is calculated by clustering analysis using BLASTClust program with similarity threshold set to percent of sequence identity.   Please view detailed explanation of sequence redundancy calculations and BLASTClust threshold settings.  Sequence redundancy calculations are based on comparison to all protein sequences in TargetDB which are in the same experimental status category and at least 20 amino acids long.

Table 6: Sequence Redundancy Statistics for Structures Released by BSGC by Year

Year	Released Structures	Number of Released Structures <30% Identity at Time of Release	Percent(%) of Released Structures <30% Identity(%) at Time of Release
<= 2000	8	4	50
2001	4	1	25
2002	8	3	38
2003	12	6	50
2004	37	14	38
2005	9	4	44
2006	7	4	57
2007	3	2	67
Total	88	38	43

Last updated: 12-02-02

Sequence redundancy is calculated by clustering analysis using BLASTClust program with similarity threshold set to percent of sequence identity.   Please view detailed explanation of sequence redundancy calculations and BLASTClust threshold settings.  Sequence redundancy calculations are based on comparison to all protein sequences in the PDB which are at least 20 amino acids long.

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